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border-box;\" \/><\/p>\n<section style=\"margin: 10px 0%;display: flex;flex-flow: row;text-align: center;justify-content: center;box-sizing: border-box;\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;flex: 0 0 0%;height: auto;line-height: 0;margin: 0px -23px 0px 0px;z-index: 2;box-sizing: border-box;\">\n<section style=\"box-sizing: border-box;\">\n<section style=\"display: inline-block;width: 16px;height: 12px;vertical-align: top;overflow: hidden;background-color: rgb(231, 215, 173);padding: 0px 2px;box-sizing: border-box;\">\n<section style=\"justify-content: center;display: flex;flex-flow: row;box-sizing: border-box;\">\n<section style=\"display: inline-block;vertical-align: top;width: 50%;align-self: flex-start;flex: 0 0 auto;box-sizing: border-box;\">\n<section style=\"margin: 4px 0% 0px;box-sizing: border-box;\">\n<section style=\"display: inline-block;width: 3px;height: 3px;vertical-align: top;overflow: hidden;border-width: 0px;border-radius: 155px;border-style: none;border-color: rgb(62, 62, 62);background-color: rgb(245, 245, 245);box-sizing: border-box;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: 50%;align-self: flex-start;flex: 0 0 auto;box-sizing: border-box;\">\n<section style=\"margin: 4px 0% 0px;box-sizing: border-box;\">\n<section style=\"display: inline-block;width: 3px;height: 3px;vertical-align: top;overflow: hidden;border-width: 0px;border-radius: 155px;border-style: none;border-color: rgb(62, 62, 62);background-color: rgb(245, 245, 245);box-sizing: border-box;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"transform: translate3d(3px, 0px, 0px);-webkit-transform: translate3d(3px, 0px, 0px);-moz-transform: translate3d(3px, 0px, 0px);-o-transform: translate3d(3px, 0px, 0px);box-sizing: border-box;\">\n<section style=\"display: inline-block;width: 0px;height: 0px;vertical-align: top;overflow: hidden;border-style: solid;border-width: 0px 0px 4px 4px;border-color: rgba(255, 255, 255, 0) rgba(255, 255, 255, 0) rgba(255, 255, 255, 0) rgb(231, 215, 173);box-sizing: border-box;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;background-color: rgb(245, 241, 224);flex: 0 0 auto;align-self: flex-start;margin: 6px 0px 0px;min-width: 10%;max-width: 100%;height: auto;box-sizing: border-box;\">\n<section style=\"margin: 8px 0% 3px;box-sizing: border-box;\">\n<section style=\"color: rgb(59, 149, 115);font-size: 15px;padding: 0px 15px;letter-spacing: 0px;text-align: justify;box-sizing: border-box;\">\n<p style=\"white-space: normal;margin: 0px;padding: 0px;box-sizing: border-box;\"><strong style=\"box-sizing: border-box;\">\u4e3b\u8981\u7684\u6279\u6b21\u6548\u5e94\u53ef\u80fd\u5305\u62ec\uff1a<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"text-align: left;justify-content: flex-start;margin: 20px 0px 10px;display: flex;flex-flow: row;box-sizing: border-box;\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;background-color: rgb(59, 149, 115);min-width: 10%;max-width: 100%;flex: 0 0 auto;height: auto;align-self: flex-start;box-sizing: border-box;\">\n<section style=\"color: rgb(245, 245, 245);text-align: center;letter-spacing: 1.2px;padding: 0px 20px;box-sizing: border-box;\">\n<p style=\"margin: 0px;padding: 0px;box-sizing: border-box;\"><strong style=\"box-sizing: border-box;\">\u6280\u672f\u6279\u6b21\u6548\u5e94\uff1a<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"white-space: normal;margin: 0px;padding: 0px;box-sizing: border-box;\">\u8fd9\u79cd\u6548\u5e94\u6e90\u81ea\u4e8e\u5b9e\u9a8c\u8bbe\u5907\u3001\u8bd5\u5242\u3001\u64cd\u4f5c\u8005\u7b49\u6280\u672f\u56e0\u7d20\u7684\u5dee\u5f02\uff0c\u53ef\u80fd\u4f1a\u5bfc\u81f4\u6570\u636e\u5728\u4e0d\u540c\u6279\u6b21\u4e4b\u95f4\u4ea7\u751f\u53d8\u5f02\u3002<br style=\"box-sizing: border-box;\" \/><\/p>\n<section style=\"text-align: left;justify-content: flex-start;margin: 20px 0px 10px;display: flex;flex-flow: row;box-sizing: border-box;\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;background-color: rgb(59, 149, 115);min-width: 10%;max-width: 100%;flex: 0 0 auto;height: auto;align-self: flex-start;box-sizing: border-box;\">\n<section style=\"color: rgb(245, 245, 245);text-align: center;letter-spacing: 1.2px;padding: 0px 20px;box-sizing: border-box;\">\n<p style=\"margin: 0px;padding: 0px;box-sizing: border-box;\"><strong style=\"box-sizing: border-box;\">\u751f\u7269\u6279\u6b21\u6548\u5e94\uff1a<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"white-space: normal;margin: 0px;padding: 0px;box-sizing: border-box;\">\u8fd9\u79cd\u6548\u5e94\u53ef\u80fd\u662f\u7531\u4e8e\u5b9e\u9a8c\u6837\u672c\u6765\u6e90\u7684\u53d8\u5316\uff0c\u5982\u4e0d\u540c\u7684\u52a8\u7269\u4e2a\u4f53\u3001\u4eba\u4f53\u6837\u672c\u3001\u7ec6\u80de\u7cfb\u7b49\uff0c\u4ee5\u53ca\u5b9e\u9a8c\u73af\u5883\u7684\u53d8\u5316\uff0c\u5982\u6e29\u5ea6\u3001\u6e7f\u5ea6\u7b49\uff0c\u5f15\u8d77\u7684\u7cfb\u7edf\u6027\u53d8\u5f02\u3002<br style=\"box-sizing: border-box;\" \/>\u65f6\u95f4\u6279\u6b21\u6548\u5e94\uff1a\u5982\u679c\u5b9e\u9a8c\u5728\u4e0d\u540c\u65f6\u95f4\u70b9\u8fdb\u884c\uff0c\u53ef\u80fd\u4f1a\u5f15\u5165\u65f6\u95f4\u76f8\u5173\u7684\u53d8\u5f02\uff0c\u5982\u5b63\u8282\u6027\u53d8\u5316\u3001\u751f\u957f\u9636\u6bb5\u53d8\u5316\u7b49<br style=\"box-sizing: border-box;\" \/><\/p>\n<section style=\"text-align: left;justify-content: flex-start;margin: 20px 0px 10px;display: flex;flex-flow: row;box-sizing: border-box;\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;background-color: rgb(59, 149, 115);min-width: 10%;max-width: 100%;flex: 0 0 auto;height: auto;align-self: flex-start;box-sizing: border-box;\">\n<section style=\"color: rgb(245, 245, 245);text-align: center;letter-spacing: 1.2px;padding: 0px 20px;box-sizing: border-box;\">\n<p style=\"margin: 0px;padding: 0px;box-sizing: border-box;\"><strong style=\"box-sizing: border-box;\">\u6570\u636e\u5904\u7406\u6279\u6b21\u6548\u5e94\uff1a<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"white-space: normal;margin: 0px;padding: 0px;box-sizing: border-box;\">\u5728\u6570\u636e\u5206\u6790\u8fc7\u7a0b\u4e2d\uff0c\u5982\u679c\u91c7\u7528\u4e86\u4e0d\u540c\u7684\u6570\u636e\u5904\u7406\u65b9\u6cd5\u3001\u53c2\u6570\u6216\u8f6f\u4ef6\u5de5\u5177\uff0c\u4e5f\u53ef\u80fd\u5bfc\u81f4\u6279\u6b21\u6548\u5e94\u3002<br style=\"box-sizing: border-box;\" \/>\u4eca\u5929\uff0c\u5927\u6d77\u54e5\u5c31\u8981\u5bf9\u5b58\u5728\u6279\u6b21\u6548\u5e94\u7684\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u8fdb\u884c\u5904\u7406\uff0c\u8ba9\u4ed6\u4eec\u53ef\u4ee5\u5b8c\u7f8e\u878d\u5408\uff01<br style=\"box-sizing: border-box;\" \/><\/p>\n<p style=\"white-space: normal;margin: 0px;padding: 0px;box-sizing: border-box;\">\u4eca\u5929\uff0c\u5927\u6d77\u54e5\u5c31\u8981\u5bf9\u5b58\u5728\u6279\u6b21\u6548\u5e94\u7684\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u8fdb\u884c\u5904\u7406\uff0c\u8ba9\u4ed6\u4eec\u53ef\u4ee5\u5b8c\u7f8e\u878d\u5408\uff01<\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#\u9996\u5148\uff0c\u6211\u4eec\u4e0b\u8f7d\u4e00\u4e0b\u5bf9\u5e94\u7684\u6570\u636e<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#\u6211\u4eec\u9009\u62e9GEO\u6570\u636e\u7684\u4e24\u4e2a\u5b58\u5728\u6279\u6b21\u6548\u5e94\u7684\u6570\u636e\u54e6\uff01<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">rm(<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">list<\/span> = ls())<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">options(stringsAsFactors = <span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">F<\/span>)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">library(GEOquery)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">eSet1 <- getGEO(<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"GSE83521\"<\/span>,<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"> destdir = <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">'.'<\/span>,<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"> getGPL = <span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">F<\/span>)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#(1)\u63d0\u53d6\u8868\u8fbe\u77e9\u9635exp<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">exp1 <- exprs(eSet1[[<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>]])<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">exp1[<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>:<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">4<\/span>,<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>:<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">4<\/span>]<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">dim<\/span>(exp1)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#\u7136\u540e\u6211\u4eec\u770b\u4e00\u4e0b\u8fd9\u4e2a\u6570\u636e\u7684\u7bb1\u578b\u56fe<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># \u4e00\u5b9a\u8981\u770bboxplot<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">boxplot(exp1,las=<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">2<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;box-sizing: border-box;\">\n<section style=\"max-width: 100%;vertical-align: middle;display: inline-block;line-height: 0;box-sizing: border-box;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.7083333333333334\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_pL1kySeAibZPQ6KsV5qdXK7DOhWWaw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSQLkf0kweibnQuoceeZFbcB6RJnB0Hia91bEUlicbpy3s3lwWWEpL1kySeAibZPQ6KsV5qdXK7DOhWWaw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"552\" style=\"vertical-align: middle;max-width: 100%;width: 100%;box-sizing: border-box;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">pd1 <- pData(eSet1[[<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>]])<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#(3)\u63d0\u53d6\u82af\u7247\u5e73\u53f0\u7f16\u53f7<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">gpl1 <- eSet1[[<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>]]@annotation<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#\u7136\u540e\u5f00\u59cb\u4e0b\u8f7d\u7b2c\u4e8c\u4e2a\u6570\u636e<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">eSet2 <- getGEO(<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"GSE89143\"<\/span>,<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"> destdir = <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">'.'<\/span>,<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"> getGPL = <span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">F<\/span>)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#(1)\u63d0\u53d6\u8868\u8fbe\u77e9\u9635exp<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">exp2 <- exprs(eSet2[[<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>]])<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">exp2[<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>:<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">4<\/span>,<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>:<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">4<\/span>]<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">dim<\/span>(exp2)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">boxplot(exp2,las=<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">2<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;box-sizing: border-box;\">\n<section style=\"max-width: 100%;vertical-align: middle;display: inline-block;line-height: 0;box-sizing: border-box;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.5824175824175825\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_pibV5BgS17BYtNbvkwl7IfpwbgQ3gw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSQLkf0kweibnQuoceeZFbcB6tVzjlw1w0QZ37XibFlwbswicLlcpibV5BgS17BYtNbvkwl7IfpwbgQ3gw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"546\" style=\"vertical-align: middle;max-width: 100%;width: 100%;box-sizing: border-box;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#\u4ece\u4e0a\u9762\u7684\u7bb1\u7ebf\u56fe\u7ed3\u679c\u53ef\u4ee5\u770b\u5230\uff0c\u6570\u503c\u7684\u8868\u8fbe\u91cf\u5e76\u4e0d\u5728\u540c\u4e00\u6761\u6c34\u5e73\u7ebf\u4e0a\uff0c\u5e76\u4e14\u6709\u6210\u8d25\u4e0a\u5343\uff0c\u4e5f\u6709\u96f6\uff0c\u5f88\u660e\u663e\u662f\u6ca1\u6709\u7ecf\u8fc7log\u7684\u3002\u8fd9\u662f\u9700\u8981\u628a\u6570\u636elog\u540e\u518d\u7528boxplot\u6765\u770b\u6570\u636e\u7684\u5206\u5e03<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#log(x+1)\u9884\u5904\u7406\u4e00\u4e0b<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">exp2 = log2(exp2+<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">boxplot(exp2,las=<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">2<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;box-sizing: border-box;\">\n<section style=\"max-width: 100%;vertical-align: middle;display: inline-block;line-height: 0;box-sizing: border-box;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.5711678832116789\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_IciclwNicNapD3royv0dLevJKspb5w.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSQLkf0kweibnQuoceeZFbcB64JgYKsNVNibz3wdTeibZ9LjYbp9sIciclwNicNapD3royv0dLevJKspb5w\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"548\" style=\"vertical-align: middle;max-width: 100%;width: 100%;box-sizing: border-box;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#\u7136\u540e\u6211\u4eec\u518d\u4f7f\u7528\u4e00\u4e2a\u5389\u5bb3\u7684\u51fd\u6570normalizeBetweenArrays<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">library(limma)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">exp2=normalizeBetweenArrays(exp2)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">boxplot(exp2,las=<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">2<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;box-sizing: border-box;\">\n<section style=\"max-width: 100%;vertical-align: middle;display: inline-block;line-height: 0;box-sizing: border-box;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.5851449275362319\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_OJib1jI7KmVzxuNyiakYp9Z8tTYicg.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSQLkf0kweibnQuoceeZFbcB6P6twaibX9Sx96cfrertqT52NVdl9OJib1jI7KmVzxuNyiakYp9Z8tTYicg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"552\" style=\"vertical-align: middle;max-width: 100%;width: 100%;box-sizing: border-box;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#\u53ef\u4ee5\u770b\u5230\uff0c\u73b0\u5728\u6570\u636e\u96c62\u7684\u6570\u636e\u90fd\u57fa\u672c\u4e0a\u5904\u4e8e\u7edf\u4e00\u8303\u56f4\u533a\u95f4\u4e86\uff0c\u53ef\u4ee5\u8fdb\u884c\u4e0b\u4e00\u6b65\u64cd\u4f5c\u4e86<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#\u63a2\u9488\u6ce8\u91ca<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#\u8fd9\u4e00\u6b65\u4e5f\u662f\u6211\u4eec\u65e5\u5e38\u4f7f\u7528GEO\u6570\u636e\u5fc5\u987b\u8981\u6709\u7684\u64cd\u4f5c\uff0c\u8fd9\u91cc\u4e5f\u987a\u4fbf\u4ecb\u7ecd\u4e00\u4e0b\u5427<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#(2)\u63d0\u53d6\u4e34\u5e8a\u4fe1\u606f<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">pd2 <- pData(eSet2[[<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>]])<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#(3)\u63d0\u53d6\u82af\u7247\u5e73\u53f0\u7f16\u53f7<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">gpl2 <- eSet2[[<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>]]@annotation<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">gpl2<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">gpl1<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#\u662f\u540c\u4e00\u4e2a\u5e73\u53f0\uff01\u5f88\u4e0d\u9519<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__keyword\" style=\"box-sizing: border-box;\">if<\/span>(<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">T<\/span>){<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"> library(GEOquery)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"> gpl<- getGEO(<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">'GPL19978'<\/span>, destdir=<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\".\"<\/span>)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"> <span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">dim<\/span>(gpl)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"> colnames(Table(gpl)) <span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#\u67e5\u4e00\u4e0b\u5217\u660e<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"> head(Table(gpl)[,<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">c<\/span>(<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>,<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">2<\/span>)])<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"> ids=Table(gpl)[,<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">c<\/span>(<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>,<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">2<\/span>)]<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"> ids <- ids[-<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">c<\/span>(<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>:<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">2<\/span>),]<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"> ids <- ids[-<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">c<\/span>(<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>:<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">13<\/span>),]<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"> save(ids,file=<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">'ids.Rdata'<\/span>)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">}<\/span><\/code><\/pre>\n<\/section>\n<p style=\"white-space: normal;margin: 0px;padding: 0px;box-sizing: border-box;\">#\u770b\u4e00\u4e0b\u5bf9\u5e94\u5173\u7cfb<\/p>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;box-sizing: border-box;\">\n<section style=\"max-width: 100%;vertical-align: middle;display: inline-block;line-height: 0;box-sizing: border-box;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.7088305489260143\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_D8MVDBzuejTXW4cZiba4HHuaGqTDRQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSQLkf0kweibnQuoceeZFbcB6fFswqvgl5hSvWDYa7eCIZxiaqHD8MVDBzuejTXW4cZiba4HHuaGqTDRQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"419\" style=\"vertical-align: middle;max-width: 100%;width: 100%;box-sizing: border-box;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<p style=\"white-space: normal;margin: 0px;padding: 0px;box-sizing: border-box;\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#\u672c\u6b21\u4f7f\u7528\u7684\u7b97\u6cd5\u662f\u652f\u6301lp\u3001distr\u4ee5\u53cacrank\uff0c\u6240\u4ee5\u4e0a\u56fe\u4e2d\u5bf9\u5e94\u7684\u6307\u6807\u90fd\u652f\u6301\u54e6\uff01<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#\u540c\u6837\u652f\u6301IBS\u6307\u6807\uff0c\u6211\u4eec\u770b\u770b\uff0c\u4e00\u884c\u641e\u5b9a<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">p$score(msrs(<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"surv.brier\"<\/span>))<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;box-sizing: border-box;\">\n<section style=\"max-width: 100%;vertical-align: middle;display: inline-block;line-height: 0;box-sizing: border-box;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.18149466192170818\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_RGkSB6dXKuwSlwqu7CZSwXDiaQVibg.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSQLkf0kweibnQuoceeZFbcB6Aje7Ft4W26sZqCzzltRhOBvyKKRGkSB6dXKuwSlwqu7CZSwXDiaQVibg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"281\" style=\"vertical-align: middle;max-width: 100%;width: 100%;box-sizing: border-box;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#\u5408\u5e76\u6570\u636e<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">x1 <- exp1[rownames(exp1) %in% ids$ID,]<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">x2 <- exp2[rownames(exp2) %in% ids$ID,]<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">boxplot(x1,las=<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">2<\/span>)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">boxplot(x2,las=<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">2<\/span>)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">cg=intersect(rownames(x1),rownames(x2))<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">x_merge=cbind(x1[cg,],x2[cg,])<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#\u6211\u4eec\u770b\u4e00\u4e0b\u5408\u5e76\u540e\u7684\u7ed3\u679c<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">boxplot(x_merge)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;box-sizing: border-box;\">\n<section style=\"max-width: 100%;vertical-align: middle;display: inline-block;line-height: 0;box-sizing: border-box;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.5247706422018349\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_yOtxWkicGQtYlu9oChPrGEfeJ2Encg.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSQLkf0kweibnQuoceeZFbcB6ialfqDib0Ac4xIG4R1bh1SlIm9UyOtxWkicGQtYlu9oChPrGEfeJ2Encg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"545\" style=\"vertical-align: middle;max-width: 100%;width: 100%;box-sizing: border-box;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#\u4e0a\u9762\u8fd9\u5f20\u56fe\uff0c\u5c31\u662f\u975e\u5e38\u660e\u663e\u7684\u770b\u5230\u4e86\uff0c\u7531\u4e8e\u540e\u9762\u7684\u4e09\u4e2a\u6837\u672c\u5c31\u662f\u6765\u81ea\u53e6\u4e00\u4e2a\u6570\u636e\u96c6\u7684\u3002\u6240\u4ee5\u8fd9\u79cd\u5c31\u662f\u8bf4\u660e\u5176\u5b58\u5728\u6279\u6b21\u6548\u5e94<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#\u5dee\u5f02\u5206\u6790\u53bb\u9664\u6279\u6b21\u6548\u5e94<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">pd1$title<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">pd2$characteristics_ch1<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">group_list <- <span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">c<\/span>(<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">rep<\/span>(<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">'tumor'<\/span>,<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">6<\/span>),<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">rep<\/span>(<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">'normal'<\/span>,<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">6<\/span>),<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">rep<\/span>(<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">c<\/span>(<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">'tumor'<\/span>, <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">'normal'<\/span>),each=<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">3<\/span>))<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">gse <- <span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">c<\/span>(<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">rep<\/span>(<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">'GSE83527'<\/span>,<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">12<\/span>),<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">rep<\/span>(<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">'GSE89143'<\/span>,<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">6<\/span>))<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">table(group_list,gse)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">dat <- x_merge<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">library(sva)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">library(limma)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">## \u4f7f\u7528 limma \u7684 removeBatchEffect \u51fd\u6570<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">dat[<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>:<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">4<\/span>,<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>:<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">4<\/span>]<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">batch <- <span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">c<\/span>(<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">rep<\/span>(<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">'GSE83521'<\/span>,<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">12<\/span>),<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">rep<\/span>(<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">'GSE89143'<\/span>,<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">6<\/span>))<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">design=model.matrix(~group_list)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">ex_b_limma <- removeBatchEffect(dat,<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"> batch = batch,<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"> design = design)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">dim<\/span>(ex_b_limma)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#\u8fd9\u4e2a\u65f6\u5019\u4e00\u5b9a\u8981\u770b boxplot\uff0c\u4e0d\u7136\u5c31\u767d\u770b\u4e86\u8fd9\u4e48\u4e45\u4e86\uff01<\/span><\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;box-sizing: border-box;\">\n<section style=\"max-width: 100%;vertical-align: middle;display: inline-block;line-height: 0;box-sizing: border-box;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.533457249070632\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/8_swUlJH0YvZfdbACeOibZIvjDtHSfUw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSQLkf0kweibnQuoceeZFbcB6Lb0EhJS9TcOiaJW4UDAfBD7RJ5swUlJH0YvZfdbACeOibZIvjDtHSfUw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"538\" style=\"vertical-align: middle;max-width: 100%;width: 100%;box-sizing: border-box;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<p style=\"white-space: normal;margin: 0px;padding: 0px;box-sizing: border-box;\">\u4ece\u4e0a\u9762\u7684\u56fe\u53ef\u4ee5\u770b\u5230\u4e86\uff0c\u53bb\u9664\u4e86\u6279\u6b21\u6548\u5e94\u540e\uff0c\u6570\u636e\u7684\u8868\u8fbe\u6c34\u5e73\u57fa\u672c\u7b26\u5408\u6b63\u5e38\u4e86\uff0c\u8fd9\u4e5f\u8bf4\u660e\u672c\u6b21\u4ee3\u7801\u5b9e\u73b0\u4e86\u6211\u4eec\u7684\u76ee\u7684\u3002\u5927\u529f\u544a\u6210\uff01<\/p>\n<p style=\"white-space: normal;margin: 0px;padding: 0px;box-sizing: border-box;\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<section style=\"display: flex;flex-flow: row;margin: 10px 0% 20px;text-align: left;justify-content: flex-start;box-sizing: border-box;\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;flex: 0 0 0%;height: auto;align-self: flex-start;line-height: 0;box-sizing: border-box;\">\n<section style=\"text-align: right;margin: 0px 0% -20px;box-sizing: border-box;\">\n<section style=\"display: inline-block;width: 8px;height: 20px;vertical-align: top;overflow: hidden;border-width: 0px;border-style: none;border-color: rgb(62, 62, 62);background-color: rgb(245, 241, 224);box-sizing: border-box;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<section style=\"text-align: center;box-sizing: border-box;\">\n<section style=\"display: inline-block;width: 16px;height: 20px;vertical-align: top;overflow: hidden;border-width: 0px;border-radius: 21px 21px 0px 0px;border-style: none;border-color: rgb(62, 62, 62);background-color: rgb(231, 215, 173);box-sizing: border-box;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;background-color: rgb(245, 241, 224);flex: 100 100 0%;align-self: flex-start;height: auto;border-right: 0px rgb(62, 62, 62);border-top-right-radius: 12px;overflow: hidden;box-shadow: rgb(231, 215, 173) 0px 6px 0px;box-sizing: border-box;\">\n<section style=\"margin: 20px 0% 30px;box-sizing: border-box;\">\n<section style=\"padding: 0px 10px;text-align: justify;box-sizing: border-box;\">\n<p style=\"white-space: normal;margin: 0px;padding: 0px;box-sizing: border-box;\">\u603b\u7ed3\u4e00\u4e0b\uff0c\u91cd\u8981\u7684\u5982\u4e0b\uff1a<br style=\"box-sizing: border-box;\" \/>\u7b2c\u4e00\u70b9\uff0c\u6211\u4eec\u8981\u7406\u89e3boxplot\u7684\u91cd\u8981\u6027\uff0c\u6765\u770b\u6570\u636e\u96c6\u662f\u5426\u9700\u8981log\uff0c\u4ee5\u4fbf\u540e\u9762\u624d\u80fd\u7528limma\u5305\u8fdb\u884c\u5dee\u5f02\u5206\u6790\uff0c\u7b2c\u4e8c\u70b9\uff0cnormalizeBetweenArrays\u53ea\u80fd\u662f\u5728\u540c\u4e00\u4e2a\u6570\u636e\u96c6\u91cc\u9762\u7528\u6765\u53bb\u9664\u6837\u672c\u7684\u5dee\u5f02\uff0c\u4e0d\u540c\u6570\u636e\u96c6\u9700\u8981\u7528limma \u7684 removeBatchEffect\u51fd\u6570\u53bb\u9664\u6279\u6b21\u6548\u5e94\u3002<br style=\"box-sizing: border-box;\" \/>\u597d\u4e86\uff0c\u4eca\u5929\u7684\u5206\u4eab\u5c31\u5230\u8fd9\u91cc\u5566\uff0c\u5927\u5bb6\u7ed3\u675f\u540e\u4e00\u5b9a\u8981\u81ea\u5df1\u52a8\u624b\u8bd5\u8bd5\u54e6\uff01\u770b\u770b\u6709\u6ca1\u6709\u65b0\u53d1\u73b0\uff01<strong>\uff08\u6700\u540e\u63a8\u8350\u4e00\u4e0b\u5927\u6d77\u54e5\u65b0\u5f00\u53d1\u7684\u96f6\u4ee3\u7801\u4e91\u751f\u4fe1\u5206\u6790\u5de5\u5177\u5e73\u53f0\u5305\u542b\u8d85\u591a\u96f6\u4ee3\u7801\u5c0f\u5de5\u5177\uff0c\u4e0a\u4f20\u6570\u636e\u4e00\u952e\u51fa\u56fe\uff0c\u611f\u5174\u8da3\u7684\u5c0f\u4f19\u4f34\u6b22\u8fce\u6765\u53c2\u89c2\u54df\uff0c\u7f51\u5740\uff1ahttp:\/\/www.biocloudservice.com\/home.html\uff09<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"border-bottom: 2px solid rgb(0, 150, 136);text-align: left;font-size: 12px;box-sizing: border-box;\">\n<p style=\"margin: 0px;padding: 0px;box-sizing: border-box;\"><a target=\"_blank\" href=\"https:\/\/mp.weixin.qq.com\/s?__biz=MzAwNjE0MDY3MQ==&mid=2650761303&idx=2&sn=6f73471d1e82c56c0b2160d0fcd32d53&scene=21#wechat_redirect\" textvalue=\"\" linktype=\"image\" imgurl=\"https:\/\/mmbiz.qpic.cn\/mmbiz_jpg\/YHGRXkSxjSSYqN0u6bwwXzLCBdlX9BXOYJyjlsib6bQ74Wibtria9gSC4sqocafb5YBQcZWdQRrtP2Xo7vaFWaecA\/0?wx_fmt=jpeg\" imgdata=\"[object Object]\" tab=\"innerlink\" data-linktype=\"1\" rel=\"noopener\"><span class=\"js_jump_icon h5_image_link\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.35083798882681566\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/9_ocafb5YBQcZWdQRrtP2Xo7vaFWaecA-3.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_jpg\/YHGRXkSxjSSYqN0u6bwwXzLCBdlX9BXOYJyjlsib6bQ74Wibtria9gSC4sqocafb5YBQcZWdQRrtP2Xo7vaFWaecA\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"895\" style=\"\" data-recalc-dims=\"1\" \/><\/span><\/a><\/p>\n<p 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[…]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/59372"}],"collection":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=59372"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/59372\/revisions"}],"predecessor-version":[{"id":59383,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/59372\/revisions\/59383"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=59372"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=59372"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=59372"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}

{"id":59372,"date":"2024-06-17T07:59:46","date_gmt":"2024-06-16T23:59:46","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=59372"},"modified":"2024-06-17T07:59:46","modified_gmt":"2024-06-16T23:59:46","slug":"%e6%95%b0%e6%8d%ae%e5%ad%98%e5%9c%a8%e6%89%b9%e6%ac%a1%e6%95%88%e5%ba%94%ef%bc%9f%e6%9d%a5%e8%bf%99%e9%87%8c%e8%ae%a9%e5%a4%a7%e6%b5%b7%e5%93%a5%e6%95%99%e4%bd%a0%e6%80%8e%e4%b9%88%e5%a4%84%e7%90%86","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=59372","title":{"rendered":"\u6570\u636e\u5b58\u5728\u6279\u6b21\u6548\u5e94\uff1f\u6765\u8fd9\u91cc\u8ba9\u5927\u6d77\u54e5\u6559\u4f60\u600e\u4e48\u5904\u7406"},"content":{"rendered":"

\n
\n<\/title><br \/>\n<meta charset=\"utf-8\"><br \/>\n<meta name=\"viewport\" content=\"width=device-width,initial-scale=1.0,maximum-scale=1.0,user-scalable=0,viewport-fit=cover\"><\/p>\n<style>\n*{margin:0;padding:0}html{-ms-text-size-adjust:100%;-webkit-text-size-adjust:100%;line-height:1.6}img{z-index:999;position:relative;max-width:100%;margin:10px 0;}body{letter-spacing:.034em}h1,h2,h3,h4,h5,h6{font-weight:400;font-size:16px}a{color:#576b95;text-decoration:none;-webkit-tap-highlight-color:rgba(0,0,0,0)}td,th{word-wrap:break-word;padding:5px 10px;border:1px solid #DDD;}table{margin-bottom:10px;border-collapse:collapse;display:table;width:100%!important;}.appmsg_skin_default .rich_media_area_primary{background-color:#fff}.appmsg_skin_default .rich_media_area_primary .weui-loadmore_line .weui-loadmore__tips{background-color:#fff}.rich_media_area_primary{padding:20px 16px 12px;background-color:#fafafa}@media (max-width:375px){.rich_media_area_primary{padding:20px 60px 15px 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translate3d(3px, 0px, 0px);-o-transform: translate3d(3px, 0px, 0px);box-sizing: border-box;\">\n<section style=\"display: inline-block;width: 0px;height: 0px;vertical-align: top;overflow: hidden;border-style: solid;border-width: 0px 0px 4px 4px;border-color: rgba(255, 255, 255, 0) rgba(255, 255, 255, 0) rgba(255, 255, 255, 0) rgb(231, 215, 173);box-sizing: border-box;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;background-color: rgb(245, 241, 224);flex: 0 0 auto;align-self: flex-start;margin: 6px 0px 0px;min-width: 10%;max-width: 100%;height: auto;box-sizing: border-box;\">\n<section style=\"margin: 8px 0% 3px;box-sizing: border-box;\">\n<section style=\"color: rgb(59, 149, 115);font-size: 15px;padding: 0px 15px;letter-spacing: 0px;text-align: justify;box-sizing: border-box;\">\n<p style=\"white-space: normal;margin: 0px;padding: 0px;box-sizing: border-box;\"><strong style=\"box-sizing: border-box;\">\u4e3b\u8981\u7684\u6279\u6b21\u6548\u5e94\u53ef\u80fd\u5305\u62ec\uff1a<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"text-align: left;justify-content: flex-start;margin: 20px 0px 10px;display: flex;flex-flow: row;box-sizing: border-box;\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;background-color: rgb(59, 149, 115);min-width: 10%;max-width: 100%;flex: 0 0 auto;height: auto;align-self: flex-start;box-sizing: border-box;\">\n<section style=\"color: rgb(245, 245, 245);text-align: center;letter-spacing: 1.2px;padding: 0px 20px;box-sizing: border-box;\">\n<p style=\"margin: 0px;padding: 0px;box-sizing: border-box;\"><strong style=\"box-sizing: border-box;\">\u6280\u672f\u6279\u6b21\u6548\u5e94\uff1a<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"white-space: normal;margin: 0px;padding: 0px;box-sizing: border-box;\">\u8fd9\u79cd\u6548\u5e94\u6e90\u81ea\u4e8e\u5b9e\u9a8c\u8bbe\u5907\u3001\u8bd5\u5242\u3001\u64cd\u4f5c\u8005\u7b49\u6280\u672f\u56e0\u7d20\u7684\u5dee\u5f02\uff0c\u53ef\u80fd\u4f1a\u5bfc\u81f4\u6570\u636e\u5728\u4e0d\u540c\u6279\u6b21\u4e4b\u95f4\u4ea7\u751f\u53d8\u5f02\u3002<br style=\"box-sizing: border-box;\" \/><\/p>\n<section style=\"text-align: left;justify-content: flex-start;margin: 20px 0px 10px;display: flex;flex-flow: row;box-sizing: border-box;\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;background-color: rgb(59, 149, 115);min-width: 10%;max-width: 100%;flex: 0 0 auto;height: auto;align-self: flex-start;box-sizing: border-box;\">\n<section style=\"color: rgb(245, 245, 245);text-align: center;letter-spacing: 1.2px;padding: 0px 20px;box-sizing: border-box;\">\n<p style=\"margin: 0px;padding: 0px;box-sizing: border-box;\"><strong style=\"box-sizing: border-box;\">\u751f\u7269\u6279\u6b21\u6548\u5e94\uff1a<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"white-space: normal;margin: 0px;padding: 0px;box-sizing: border-box;\">\u8fd9\u79cd\u6548\u5e94\u53ef\u80fd\u662f\u7531\u4e8e\u5b9e\u9a8c\u6837\u672c\u6765\u6e90\u7684\u53d8\u5316\uff0c\u5982\u4e0d\u540c\u7684\u52a8\u7269\u4e2a\u4f53\u3001\u4eba\u4f53\u6837\u672c\u3001\u7ec6\u80de\u7cfb\u7b49\uff0c\u4ee5\u53ca\u5b9e\u9a8c\u73af\u5883\u7684\u53d8\u5316\uff0c\u5982\u6e29\u5ea6\u3001\u6e7f\u5ea6\u7b49\uff0c\u5f15\u8d77\u7684\u7cfb\u7edf\u6027\u53d8\u5f02\u3002<br style=\"box-sizing: border-box;\" \/>\u65f6\u95f4\u6279\u6b21\u6548\u5e94\uff1a\u5982\u679c\u5b9e\u9a8c\u5728\u4e0d\u540c\u65f6\u95f4\u70b9\u8fdb\u884c\uff0c\u53ef\u80fd\u4f1a\u5f15\u5165\u65f6\u95f4\u76f8\u5173\u7684\u53d8\u5f02\uff0c\u5982\u5b63\u8282\u6027\u53d8\u5316\u3001\u751f\u957f\u9636\u6bb5\u53d8\u5316\u7b49<br style=\"box-sizing: border-box;\" \/><\/p>\n<section style=\"text-align: left;justify-content: flex-start;margin: 20px 0px 10px;display: flex;flex-flow: row;box-sizing: border-box;\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;background-color: rgb(59, 149, 115);min-width: 10%;max-width: 100%;flex: 0 0 auto;height: auto;align-self: flex-start;box-sizing: border-box;\">\n<section style=\"color: rgb(245, 245, 245);text-align: center;letter-spacing: 1.2px;padding: 0px 20px;box-sizing: border-box;\">\n<p style=\"margin: 0px;padding: 0px;box-sizing: border-box;\"><strong style=\"box-sizing: border-box;\">\u6570\u636e\u5904\u7406\u6279\u6b21\u6548\u5e94\uff1a<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"white-space: normal;margin: 0px;padding: 0px;box-sizing: border-box;\">\u5728\u6570\u636e\u5206\u6790\u8fc7\u7a0b\u4e2d\uff0c\u5982\u679c\u91c7\u7528\u4e86\u4e0d\u540c\u7684\u6570\u636e\u5904\u7406\u65b9\u6cd5\u3001\u53c2\u6570\u6216\u8f6f\u4ef6\u5de5\u5177\uff0c\u4e5f\u53ef\u80fd\u5bfc\u81f4\u6279\u6b21\u6548\u5e94\u3002<br style=\"box-sizing: border-box;\" \/>\u4eca\u5929\uff0c\u5927\u6d77\u54e5\u5c31\u8981\u5bf9\u5b58\u5728\u6279\u6b21\u6548\u5e94\u7684\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u8fdb\u884c\u5904\u7406\uff0c\u8ba9\u4ed6\u4eec\u53ef\u4ee5\u5b8c\u7f8e\u878d\u5408\uff01<br style=\"box-sizing: border-box;\" \/><\/p>\n<p style=\"white-space: normal;margin: 0px;padding: 0px;box-sizing: border-box;\">\u4eca\u5929\uff0c\u5927\u6d77\u54e5\u5c31\u8981\u5bf9\u5b58\u5728\u6279\u6b21\u6548\u5e94\u7684\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u8fdb\u884c\u5904\u7406\uff0c\u8ba9\u4ed6\u4eec\u53ef\u4ee5\u5b8c\u7f8e\u878d\u5408\uff01<\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#\u9996\u5148\uff0c\u6211\u4eec\u4e0b\u8f7d\u4e00\u4e0b\u5bf9\u5e94\u7684\u6570\u636e<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#\u6211\u4eec\u9009\u62e9GEO\u6570\u636e\u7684\u4e24\u4e2a\u5b58\u5728\u6279\u6b21\u6548\u5e94\u7684\u6570\u636e\u54e6\uff01<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">rm(<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">list<\/span> = ls())<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">options(stringsAsFactors = <span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">F<\/span>)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">library(GEOquery)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">eSet1 <- getGEO(<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"GSE83521\"<\/span>,<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"> destdir = <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">'.'<\/span>,<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"> getGPL = <span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">F<\/span>)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#(1)\u63d0\u53d6\u8868\u8fbe\u77e9\u9635exp<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">exp1 <- exprs(eSet1[[<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>]])<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">exp1[<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>:<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">4<\/span>,<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>:<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">4<\/span>]<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">dim<\/span>(exp1)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#\u7136\u540e\u6211\u4eec\u770b\u4e00\u4e0b\u8fd9\u4e2a\u6570\u636e\u7684\u7bb1\u578b\u56fe<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># \u4e00\u5b9a\u8981\u770bboxplot<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">boxplot(exp1,las=<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">2<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;box-sizing: border-box;\">\n<section style=\"max-width: 100%;vertical-align: middle;display: inline-block;line-height: 0;box-sizing: border-box;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.7083333333333334\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_pL1kySeAibZPQ6KsV5qdXK7DOhWWaw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSQLkf0kweibnQuoceeZFbcB6RJnB0Hia91bEUlicbpy3s3lwWWEpL1kySeAibZPQ6KsV5qdXK7DOhWWaw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"552\" style=\"vertical-align: middle;max-width: 100%;width: 100%;box-sizing: border-box;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">pd1 <- pData(eSet1[[<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>]])<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#(3)\u63d0\u53d6\u82af\u7247\u5e73\u53f0\u7f16\u53f7<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">gpl1 <- eSet1[[<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>]]@annotation<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#\u7136\u540e\u5f00\u59cb\u4e0b\u8f7d\u7b2c\u4e8c\u4e2a\u6570\u636e<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">eSet2 <- getGEO(<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"GSE89143\"<\/span>,<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"> destdir = <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">'.'<\/span>,<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"> getGPL = <span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">F<\/span>)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#(1)\u63d0\u53d6\u8868\u8fbe\u77e9\u9635exp<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">exp2 <- exprs(eSet2[[<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>]])<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">exp2[<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>:<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">4<\/span>,<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>:<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">4<\/span>]<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">dim<\/span>(exp2)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">boxplot(exp2,las=<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">2<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;box-sizing: border-box;\">\n<section style=\"max-width: 100%;vertical-align: middle;display: inline-block;line-height: 0;box-sizing: border-box;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.5824175824175825\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_pibV5BgS17BYtNbvkwl7IfpwbgQ3gw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSQLkf0kweibnQuoceeZFbcB6tVzjlw1w0QZ37XibFlwbswicLlcpibV5BgS17BYtNbvkwl7IfpwbgQ3gw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"546\" style=\"vertical-align: middle;max-width: 100%;width: 100%;box-sizing: border-box;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#\u4ece\u4e0a\u9762\u7684\u7bb1\u7ebf\u56fe\u7ed3\u679c\u53ef\u4ee5\u770b\u5230\uff0c\u6570\u503c\u7684\u8868\u8fbe\u91cf\u5e76\u4e0d\u5728\u540c\u4e00\u6761\u6c34\u5e73\u7ebf\u4e0a\uff0c\u5e76\u4e14\u6709\u6210\u8d25\u4e0a\u5343\uff0c\u4e5f\u6709\u96f6\uff0c\u5f88\u660e\u663e\u662f\u6ca1\u6709\u7ecf\u8fc7log\u7684\u3002\u8fd9\u662f\u9700\u8981\u628a\u6570\u636elog\u540e\u518d\u7528boxplot\u6765\u770b\u6570\u636e\u7684\u5206\u5e03<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#log(x+1)\u9884\u5904\u7406\u4e00\u4e0b<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">exp2 = log2(exp2+<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">boxplot(exp2,las=<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">2<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;box-sizing: border-box;\">\n<section style=\"max-width: 100%;vertical-align: middle;display: inline-block;line-height: 0;box-sizing: border-box;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.5711678832116789\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_IciclwNicNapD3royv0dLevJKspb5w.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSQLkf0kweibnQuoceeZFbcB64JgYKsNVNibz3wdTeibZ9LjYbp9sIciclwNicNapD3royv0dLevJKspb5w\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"548\" style=\"vertical-align: middle;max-width: 100%;width: 100%;box-sizing: border-box;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#\u7136\u540e\u6211\u4eec\u518d\u4f7f\u7528\u4e00\u4e2a\u5389\u5bb3\u7684\u51fd\u6570normalizeBetweenArrays<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">library(limma)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">exp2=normalizeBetweenArrays(exp2)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">boxplot(exp2,las=<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">2<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;box-sizing: border-box;\">\n<section style=\"max-width: 100%;vertical-align: middle;display: inline-block;line-height: 0;box-sizing: border-box;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.5851449275362319\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_OJib1jI7KmVzxuNyiakYp9Z8tTYicg.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSQLkf0kweibnQuoceeZFbcB6P6twaibX9Sx96cfrertqT52NVdl9OJib1jI7KmVzxuNyiakYp9Z8tTYicg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"552\" style=\"vertical-align: middle;max-width: 100%;width: 100%;box-sizing: border-box;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#\u53ef\u4ee5\u770b\u5230\uff0c\u73b0\u5728\u6570\u636e\u96c62\u7684\u6570\u636e\u90fd\u57fa\u672c\u4e0a\u5904\u4e8e\u7edf\u4e00\u8303\u56f4\u533a\u95f4\u4e86\uff0c\u53ef\u4ee5\u8fdb\u884c\u4e0b\u4e00\u6b65\u64cd\u4f5c\u4e86<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#\u63a2\u9488\u6ce8\u91ca<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#\u8fd9\u4e00\u6b65\u4e5f\u662f\u6211\u4eec\u65e5\u5e38\u4f7f\u7528GEO\u6570\u636e\u5fc5\u987b\u8981\u6709\u7684\u64cd\u4f5c\uff0c\u8fd9\u91cc\u4e5f\u987a\u4fbf\u4ecb\u7ecd\u4e00\u4e0b\u5427<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#(2)\u63d0\u53d6\u4e34\u5e8a\u4fe1\u606f<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">pd2 <- pData(eSet2[[<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>]])<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#(3)\u63d0\u53d6\u82af\u7247\u5e73\u53f0\u7f16\u53f7<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">gpl2 <- eSet2[[<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>]]@annotation<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">gpl2<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">gpl1<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#\u662f\u540c\u4e00\u4e2a\u5e73\u53f0\uff01\u5f88\u4e0d\u9519<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__keyword\" style=\"box-sizing: border-box;\">if<\/span>(<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">T<\/span>){<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"> library(GEOquery)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"> gpl<- getGEO(<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">'GPL19978'<\/span>, destdir=<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\".\"<\/span>)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"> <span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">dim<\/span>(gpl)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"> colnames(Table(gpl)) <span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#\u67e5\u4e00\u4e0b\u5217\u660e<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"> head(Table(gpl)[,<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">c<\/span>(<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>,<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">2<\/span>)])<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"> ids=Table(gpl)[,<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">c<\/span>(<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>,<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">2<\/span>)]<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"> ids <- ids[-<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">c<\/span>(<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>:<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">2<\/span>),]<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"> ids <- ids[-<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">c<\/span>(<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>:<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">13<\/span>),]<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"> save(ids,file=<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">'ids.Rdata'<\/span>)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">}<\/span><\/code><\/pre>\n<\/section>\n<p style=\"white-space: normal;margin: 0px;padding: 0px;box-sizing: border-box;\">#\u770b\u4e00\u4e0b\u5bf9\u5e94\u5173\u7cfb<\/p>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;box-sizing: border-box;\">\n<section style=\"max-width: 100%;vertical-align: middle;display: inline-block;line-height: 0;box-sizing: border-box;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.7088305489260143\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_D8MVDBzuejTXW4cZiba4HHuaGqTDRQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSQLkf0kweibnQuoceeZFbcB6fFswqvgl5hSvWDYa7eCIZxiaqHD8MVDBzuejTXW4cZiba4HHuaGqTDRQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"419\" style=\"vertical-align: middle;max-width: 100%;width: 100%;box-sizing: border-box;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<p style=\"white-space: normal;margin: 0px;padding: 0px;box-sizing: border-box;\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#\u672c\u6b21\u4f7f\u7528\u7684\u7b97\u6cd5\u662f\u652f\u6301lp\u3001distr\u4ee5\u53cacrank\uff0c\u6240\u4ee5\u4e0a\u56fe\u4e2d\u5bf9\u5e94\u7684\u6307\u6807\u90fd\u652f\u6301\u54e6\uff01<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#\u540c\u6837\u652f\u6301IBS\u6307\u6807\uff0c\u6211\u4eec\u770b\u770b\uff0c\u4e00\u884c\u641e\u5b9a<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">p$score(msrs(<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"surv.brier\"<\/span>))<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;box-sizing: border-box;\">\n<section style=\"max-width: 100%;vertical-align: middle;display: inline-block;line-height: 0;box-sizing: border-box;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.18149466192170818\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_RGkSB6dXKuwSlwqu7CZSwXDiaQVibg.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSQLkf0kweibnQuoceeZFbcB6Aje7Ft4W26sZqCzzltRhOBvyKKRGkSB6dXKuwSlwqu7CZSwXDiaQVibg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"281\" style=\"vertical-align: middle;max-width: 100%;width: 100%;box-sizing: border-box;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#\u5408\u5e76\u6570\u636e<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">x1 <- exp1[rownames(exp1) %in% ids$ID,]<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">x2 <- exp2[rownames(exp2) %in% ids$ID,]<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">boxplot(x1,las=<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">2<\/span>)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">boxplot(x2,las=<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">2<\/span>)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">cg=intersect(rownames(x1),rownames(x2))<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">x_merge=cbind(x1[cg,],x2[cg,])<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#\u6211\u4eec\u770b\u4e00\u4e0b\u5408\u5e76\u540e\u7684\u7ed3\u679c<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">boxplot(x_merge)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;box-sizing: border-box;\">\n<section style=\"max-width: 100%;vertical-align: middle;display: inline-block;line-height: 0;box-sizing: border-box;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.5247706422018349\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_yOtxWkicGQtYlu9oChPrGEfeJ2Encg.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSQLkf0kweibnQuoceeZFbcB6ialfqDib0Ac4xIG4R1bh1SlIm9UyOtxWkicGQtYlu9oChPrGEfeJ2Encg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"545\" style=\"vertical-align: middle;max-width: 100%;width: 100%;box-sizing: border-box;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#\u4e0a\u9762\u8fd9\u5f20\u56fe\uff0c\u5c31\u662f\u975e\u5e38\u660e\u663e\u7684\u770b\u5230\u4e86\uff0c\u7531\u4e8e\u540e\u9762\u7684\u4e09\u4e2a\u6837\u672c\u5c31\u662f\u6765\u81ea\u53e6\u4e00\u4e2a\u6570\u636e\u96c6\u7684\u3002\u6240\u4ee5\u8fd9\u79cd\u5c31\u662f\u8bf4\u660e\u5176\u5b58\u5728\u6279\u6b21\u6548\u5e94<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#\u5dee\u5f02\u5206\u6790\u53bb\u9664\u6279\u6b21\u6548\u5e94<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">pd1$title<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">pd2$characteristics_ch1<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">group_list <- <span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">c<\/span>(<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">rep<\/span>(<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">'tumor'<\/span>,<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">6<\/span>),<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">rep<\/span>(<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">'normal'<\/span>,<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">6<\/span>),<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">rep<\/span>(<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">c<\/span>(<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">'tumor'<\/span>, <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">'normal'<\/span>),each=<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">3<\/span>))<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">gse <- <span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">c<\/span>(<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">rep<\/span>(<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">'GSE83527'<\/span>,<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">12<\/span>),<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">rep<\/span>(<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">'GSE89143'<\/span>,<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">6<\/span>))<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">table(group_list,gse)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">dat <- x_merge<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">library(sva)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">library(limma)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">## \u4f7f\u7528 limma \u7684 removeBatchEffect \u51fd\u6570<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">dat[<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>:<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">4<\/span>,<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>:<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">4<\/span>]<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">batch <- <span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">c<\/span>(<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">rep<\/span>(<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">'GSE83521'<\/span>,<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">12<\/span>),<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">rep<\/span>(<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">'GSE89143'<\/span>,<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">6<\/span>))<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">design=model.matrix(~group_list)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">ex_b_limma <- removeBatchEffect(dat,<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"> batch = batch,<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"> design = design)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">dim<\/span>(ex_b_limma)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\">#\u8fd9\u4e2a\u65f6\u5019\u4e00\u5b9a\u8981\u770b boxplot\uff0c\u4e0d\u7136\u5c31\u767d\u770b\u4e86\u8fd9\u4e48\u4e45\u4e86\uff01<\/span><\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;box-sizing: border-box;\">\n<section style=\"max-width: 100%;vertical-align: middle;display: inline-block;line-height: 0;box-sizing: border-box;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.533457249070632\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/8_swUlJH0YvZfdbACeOibZIvjDtHSfUw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSQLkf0kweibnQuoceeZFbcB6Lb0EhJS9TcOiaJW4UDAfBD7RJ5swUlJH0YvZfdbACeOibZIvjDtHSfUw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"538\" style=\"vertical-align: middle;max-width: 100%;width: 100%;box-sizing: border-box;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<p style=\"white-space: normal;margin: 0px;padding: 0px;box-sizing: border-box;\">\u4ece\u4e0a\u9762\u7684\u56fe\u53ef\u4ee5\u770b\u5230\u4e86\uff0c\u53bb\u9664\u4e86\u6279\u6b21\u6548\u5e94\u540e\uff0c\u6570\u636e\u7684\u8868\u8fbe\u6c34\u5e73\u57fa\u672c\u7b26\u5408\u6b63\u5e38\u4e86\uff0c\u8fd9\u4e5f\u8bf4\u660e\u672c\u6b21\u4ee3\u7801\u5b9e\u73b0\u4e86\u6211\u4eec\u7684\u76ee\u7684\u3002\u5927\u529f\u544a\u6210\uff01<\/p>\n<p style=\"white-space: normal;margin: 0px;padding: 0px;box-sizing: border-box;\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<section style=\"display: flex;flex-flow: row;margin: 10px 0% 20px;text-align: left;justify-content: flex-start;box-sizing: border-box;\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;flex: 0 0 0%;height: auto;align-self: flex-start;line-height: 0;box-sizing: border-box;\">\n<section style=\"text-align: right;margin: 0px 0% -20px;box-sizing: border-box;\">\n<section style=\"display: inline-block;width: 8px;height: 20px;vertical-align: top;overflow: hidden;border-width: 0px;border-style: none;border-color: rgb(62, 62, 62);background-color: rgb(245, 241, 224);box-sizing: border-box;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<section style=\"text-align: center;box-sizing: border-box;\">\n<section style=\"display: inline-block;width: 16px;height: 20px;vertical-align: top;overflow: hidden;border-width: 0px;border-radius: 21px 21px 0px 0px;border-style: none;border-color: rgb(62, 62, 62);background-color: rgb(231, 215, 173);box-sizing: border-box;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;background-color: rgb(245, 241, 224);flex: 100 100 0%;align-self: flex-start;height: auto;border-right: 0px rgb(62, 62, 62);border-top-right-radius: 12px;overflow: hidden;box-shadow: rgb(231, 215, 173) 0px 6px 0px;box-sizing: border-box;\">\n<section style=\"margin: 20px 0% 30px;box-sizing: border-box;\">\n<section style=\"padding: 0px 10px;text-align: justify;box-sizing: border-box;\">\n<p style=\"white-space: normal;margin: 0px;padding: 0px;box-sizing: border-box;\">\u603b\u7ed3\u4e00\u4e0b\uff0c\u91cd\u8981\u7684\u5982\u4e0b\uff1a<br style=\"box-sizing: border-box;\" \/>\u7b2c\u4e00\u70b9\uff0c\u6211\u4eec\u8981\u7406\u89e3boxplot\u7684\u91cd\u8981\u6027\uff0c\u6765\u770b\u6570\u636e\u96c6\u662f\u5426\u9700\u8981log\uff0c\u4ee5\u4fbf\u540e\u9762\u624d\u80fd\u7528limma\u5305\u8fdb\u884c\u5dee\u5f02\u5206\u6790\uff0c\u7b2c\u4e8c\u70b9\uff0cnormalizeBetweenArrays\u53ea\u80fd\u662f\u5728\u540c\u4e00\u4e2a\u6570\u636e\u96c6\u91cc\u9762\u7528\u6765\u53bb\u9664\u6837\u672c\u7684\u5dee\u5f02\uff0c\u4e0d\u540c\u6570\u636e\u96c6\u9700\u8981\u7528limma \u7684 removeBatchEffect\u51fd\u6570\u53bb\u9664\u6279\u6b21\u6548\u5e94\u3002<br style=\"box-sizing: border-box;\" \/>\u597d\u4e86\uff0c\u4eca\u5929\u7684\u5206\u4eab\u5c31\u5230\u8fd9\u91cc\u5566\uff0c\u5927\u5bb6\u7ed3\u675f\u540e\u4e00\u5b9a\u8981\u81ea\u5df1\u52a8\u624b\u8bd5\u8bd5\u54e6\uff01\u770b\u770b\u6709\u6ca1\u6709\u65b0\u53d1\u73b0\uff01<strong>\uff08\u6700\u540e\u63a8\u8350\u4e00\u4e0b\u5927\u6d77\u54e5\u65b0\u5f00\u53d1\u7684\u96f6\u4ee3\u7801\u4e91\u751f\u4fe1\u5206\u6790\u5de5\u5177\u5e73\u53f0\u5305\u542b\u8d85\u591a\u96f6\u4ee3\u7801\u5c0f\u5de5\u5177\uff0c\u4e0a\u4f20\u6570\u636e\u4e00\u952e\u51fa\u56fe\uff0c\u611f\u5174\u8da3\u7684\u5c0f\u4f19\u4f34\u6b22\u8fce\u6765\u53c2\u89c2\u54df\uff0c\u7f51\u5740\uff1ahttp:\/\/www.biocloudservice.com\/home.html\uff09<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"border-bottom: 2px solid rgb(0, 150, 136);text-align: left;font-size: 12px;box-sizing: border-box;\">\n<p style=\"margin: 0px;padding: 0px;box-sizing: border-box;\"><a target=\"_blank\" 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